Upgrade from 1.4.0.1

[rchouinard]

I've been asked to upgrade a Magento installation due to malicious JavaScript injections constantly taking place. The installation is quite old at 1.4.0.1, unfortunately.

The main issue is that this version uses the old PEAR repositories to manage upgrades, and those are no longer available. 

Without those repositories, what options do I have to go to 1.4.2.0 and then up the chain to 1.9?

[Tom Robertshaw]

You could try downloading the latest version of Magento 1.9 manually (zip/tar.gz) and then copying over the top of your installation. This is definitely something I would do in a development environment as there are going to be a number of issues that you'll need to resolve. 

Here's an official upgrade guide from Magento which should be useful: http://devdocs.magento.com/guides/m1x/install/installing_upgrade_details.html